Unable to install BiocManager
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@34d380a0
Last seen 12 months ago
Germany

Hello, I am trying to install various packages in my hpc, however none of them are getting installed. I have 3 versions of R on the cluster, and in none of them BiocManager or any other tool is installing.

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 

Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib:
  cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES'
Warning message:
package 'BiocManager' is not available for this version of R

Seurat, liana, none of the packages are available.

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
# please also include the results of running the following in an R session 

sessionInfo()                      
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.7 (Green Obsidian)

Matrix products: default
BLAS:   /cm/shared/apps/R4.1.2/lib64/R/lib/libRblas.so
LAPACK: /cm/shared/apps/R4.1.2/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=C                 LC_NUMERIC=C              
 [3] LC_TIME=en_US.utf-8        LC_COLLATE=en_US.utf-8    
 [5] LC_MONETARY=en_US.utf-8    LC_MESSAGES=en_US.utf-8   
 [7] LC_PAPER=en_US.utf-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.utf-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2
Biocmanager R • 889 views
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Just a thought: does this also happen if you select another mirror (thus not the Uni Munster)? It looks they have an issue with a certificate that expired recently.

Also note that seurat and liana are not Bioconductor packages.

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Thank you for your response. umm okay, maybe. I will try other mirrors as well. I tried 2-3 of them.

Yes Seurat and liana are not bioconductor packages. I am generally trying to install it for other packages. For liana I get Error: Failed to install 'unknown package' from GitHub: Line starting 'Config/testthat/edit ...' is malformed! this error. So any package I install from GitHub I have this issue.

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Have you tried using the more recent version of R?

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Switch on and off R (or Rstudio)! Give it a try again. remove also history with rm(list = ls())

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